[proofplan]
The proof has two ingredients. First, the Kähler commutation identities express the formal adjoints of $\partial_E$ and $\bar\partial_E$ through commutators with $\Lambda$. Second, the curvature identity $\nabla_E^2=\partial_E\bar\partial_E+\bar\partial_E\partial_E=\Theta_h(E)$ converts the difference of the two Laplacians into the curvature commutator. The integral identity follows by taking the $L^2$ inner product with $u$ and using the definition of formal adjoint.
[/proofplan]
[step:Establish the Kähler commutation identities for the Chern connection]
We first prove the operator identities
\begin{align*}
\bar\partial_E^*=-i[\Lambda,\partial_E],
\qquad
\partial_E^*=i[\Lambda,\bar\partial_E]
\end{align*}
on compactly supported smooth $E$-valued forms.
Fix a point $x_0\in X$. By the local normal-coordinate construction for Kähler metrics, choose a holomorphic coordinate chart $(U;z_1,\dots,z_n)$ centered at $x_0$ such that
\begin{align*}
\omega_{x_0}=i\sum_{j=1}^n dz_j\wedge d\bar z_j
\end{align*}
and the first derivatives of the metric coefficients in these coordinates vanish at $x_0$. Starting from any local holomorphic frame of $E$ over $U$, apply a constant unitary change of frame to make the Hermitian matrix $h_{\alpha\bar\beta}(x_0)$ equal to the identity, and then apply a holomorphic linear correction with prescribed first jet to make $\partial h_{\alpha\bar\beta}(x_0)=0$. In this adjusted holomorphic frame $(e_1,\dots,e_r)$, the Chern connection one-form $h^{-1}\partial h$ vanishes at $x_0$. The vanishing of the connection one-form removes the lower-order connection terms at $x_0$, and the vanishing of the first derivatives of the metric coefficients removes the lower-order terms produced by differentiating the variable-coefficient operator $\Lambda$ at $x_0$.
For each $1\leq j\leq n$, define the exterior multiplication operators on the local bundle of $E$-valued forms by
\begin{align*}
\varepsilon_j:\mathcal A^{\bullet,\bullet}(U,E)&\to \mathcal A^{\bullet+1,\bullet}(U,E),
&\alpha&\mapsto dz_j\wedge \alpha,\\
\bar\varepsilon_j:\mathcal A^{\bullet,\bullet}(U,E)&\to \mathcal A^{\bullet,\bullet+1}(U,E),
&\alpha&\mapsto d\bar z_j\wedge \alpha.
\end{align*}
Let $\iota_j$ and $\bar\iota_j$ denote their pointwise Hermitian adjoints with respect to the Hermitian metric determined by $\omega_{x_0}$ and $h_{x_0}$. With the normalization $\omega_{x_0}=i\sum_j dz_j\wedge d\bar z_j$, the adjoint Lefschetz operator at $x_0$ is
\begin{align*}
\Lambda=-i\sum_{j=1}^n \bar\iota_j\iota_j.
\end{align*}
The exterior algebra relations give
\begin{align*}
[\Lambda,\varepsilon_j]=-i\bar\iota_j,
\qquad
[\Lambda,\bar\varepsilon_j]=i\iota_j.
\end{align*}
At $x_0$, writing $\nabla_j$ for covariant differentiation in the $\partial/\partial z_j$ direction and $\nabla_{\bar j}$ for covariant differentiation in the $\partial/\partial\bar z_j$ direction,
\begin{align*}
\partial_E=\sum_{j=1}^n \varepsilon_j\nabla_j,
\qquad
\bar\partial_E=\sum_{j=1}^n \bar\varepsilon_j\nabla_{\bar j}.
\end{align*}
Evaluating the coefficient formulas for the formal adjoint differential operators at $x_0$, the normalizations above give
\begin{align*}
\partial_E^*=-\sum_{j=1}^n \iota_j\nabla_{\bar j},
\qquad
\bar\partial_E^*=-\sum_{j=1}^n \bar\iota_j\nabla_j.
\end{align*}
Therefore
\begin{align*}
[\Lambda,\partial_E]
&=
\sum_{j=1}^n [\Lambda,\varepsilon_j]\nabla_j
=
-i\sum_{j=1}^n \bar\iota_j\nabla_j
=
i\bar\partial_E^*,
\\
[\Lambda,\bar\partial_E]
&=
\sum_{j=1}^n [\Lambda,\bar\varepsilon_j]\nabla_{\bar j}
=
i\sum_{j=1}^n \iota_j\nabla_{\bar j}
=
-i\partial_E^*.
\end{align*}
Hence $\bar\partial_E^*=-i[\Lambda,\partial_E]$ and $\partial_E^*=i[\Lambda,\bar\partial_E]$ at $x_0$. Since $x_0$ was arbitrary and both sides are globally defined first-order differential operators, the identities hold globally on compactly supported smooth $E$-valued forms.
[/step]
[step:Convert the difference of Laplacians into the curvature commutator]
Set
\begin{align*}
A:=\partial_E,
\qquad
B:=\bar\partial_E.
\end{align*}
All commutators in this step are operator commutators on the common domain $\mathcal A_c^{\bullet,\bullet}(X,E)$ of compactly supported smooth $E$-valued forms.
By the identities just proved,
\begin{align*}
B^*=-i[\Lambda,A],
\qquad
A^*=i[\Lambda,B].
\end{align*}
Using these identities in the definitions of the Laplacians gives
\begin{align*}
\Delta_{\bar\partial_E}
&=
BB^*+B^*B
=
-i\bigl(B[\Lambda,A]+[\Lambda,A]B\bigr),
\\
\Delta_{\partial_E}
&=
AA^*+A^*A
=
i\bigl(A[\Lambda,B]+[\Lambda,B]A\bigr).
\end{align*}
Expanding the commutators,
\begin{align*}
\Delta_{\bar\partial_E}
&=
-i\bigl(B\Lambda A-BA\Lambda+\Lambda AB-A\Lambda B\bigr),
\\
\Delta_{\partial_E}
&=
i\bigl(A\Lambda B-AB\Lambda+\Lambda BA-B\Lambda A\bigr).
\end{align*}
Subtracting the second identity from the first, the terms $B\Lambda A$ and $A\Lambda B$ cancel, and we obtain
\begin{align*}
\Delta_{\bar\partial_E}-\Delta_{\partial_E}
&=
i(BA+AB)\Lambda-i\Lambda(AB+BA).
\end{align*}
The curvature of the [Chern connection](/page/Chern%20Connection) is
\begin{align*}
\nabla_E^2
=
(\partial_E+\bar\partial_E)^2
=
\partial_E^2+\partial_E\bar\partial_E+\bar\partial_E\partial_E+\bar\partial_E^2.
\end{align*}
The holomorphic structure is integrable, so $\bar\partial_E^2=0$. The curvature of the Chern connection has type $(1,1)$, so its $(2,0)$ component is zero; since the $(2,0)$ component of $\nabla_E^2$ is $\partial_E^2$, we also have $\partial_E^2=0$. Hence
\begin{align*}
\nabla_E^2
=
\partial_E\bar\partial_E+\bar\partial_E\partial_E
=
AB+BA.
\end{align*}
By the statement's definition $\Theta_h(E)=\nabla_E^2$, the operator $AB+BA$ is $\Theta_h(E)$ acting by wedge product of the $\operatorname{End}E$-valued $(1,1)$-form together with the endomorphism action on $E$. Therefore
\begin{align*}
\Delta_{\bar\partial_E}-\Delta_{\partial_E}
&=
i\Theta_h(E)\Lambda-\Lambda i\Theta_h(E)
=
[i\Theta_h(E),\Lambda].
\end{align*}
This proves
\begin{align*}
\Delta_{\bar\partial_E}
=
\Delta_{\partial_E}+[i\Theta_h(E),\Lambda].
\end{align*}
[/step]
[step:Take the global inner product on a compact Kähler manifold]
Assume now that $X$ is compact, and let $u\in \mathcal A^{\bullet,\bullet}(X,E)$ be smooth. Since $X$ has no boundary and is compact, the formal adjoints $\partial_E^*$ and $\bar\partial_E^*$ are the Hilbert-space adjoints with respect to the $L^2$ inner product induced by $\omega$ and $h$. Hence
\begin{align*}
(\Delta_{\bar\partial_E}u,u)_{L^2}
&=
(\bar\partial_E\bar\partial_E^*u,u)_{L^2}
+
(\bar\partial_E^*\bar\partial_Eu,u)_{L^2}
\\
&=
\|\bar\partial_E^*u\|_{L^2}^2
+
\|\bar\partial_Eu\|_{L^2}^2,
\end{align*}
and likewise
\begin{align*}
(\Delta_{\partial_E}u,u)_{L^2}
=
\|\partial_E^*u\|_{L^2}^2
+
\|\partial_Eu\|_{L^2}^2.
\end{align*}
Taking the $L^2$ inner product of
\begin{align*}
\Delta_{\bar\partial_E}u
=
\Delta_{\partial_E}u+[i\Theta_h(E),\Lambda]u
\end{align*}
with $u$ gives
\begin{align*}
\|\bar\partial_Eu\|_{L^2}^2+\|\bar\partial_E^*u\|_{L^2}^2
=
\|\partial_Eu\|_{L^2}^2+\|\partial_E^*u\|_{L^2}^2
+
([i\Theta_h(E),\Lambda]u,u)_{L^2}.
\end{align*}
This is the asserted Bochner–Kodaira–Nakano identity.
[/step]